Yes. If a client uses a suffix (Jr./SR./II/III), the users preparing the return will need to remove the suffixes or it could throw off KBA and not allow the client to pass authentication.
The tax return itself does not need to be changed. The user will just need to remove the suffix from the taxpayer's name in the Client Info Tab when processing the return. If the return has already been delivered, the green 'Edit Client Info' button in the Action menu for that return can be used to remove the suffix.